Each game i try on pcsx sometimes gives strange fps drops for about half-sec, i.e.
Persona 3 FES - sometimes in videos and always then I do first attack/magic cast/scan etc.
Guilty Gear AC+ - in battle (most annoying) and in character selection
Dark Cloud 2 - when I do a first attack
Final Fantasy X - in videos and very often with spell casts

Except those freezes, games work perfectly with 60 fps, I'm only using "2+ cores" hack, other settings is default.
Tested it on several revisions, but same problem. :\

Tried recommended hacks and it worked! But after I rebooted PC it's started fps droping again. ><
Probably more like my system software problem. :\
And it doesn't give fps drops in FF7oC or Kingdom Hearts. Weird.

I don't think 53 degrees and 15% CPU usage can affect perfomance. :|
Well, sorta some progress with final fantasy x (didn't test other games) : no fps drops in movies and spell casts for about 1-2 hours, after that it starts again -.- but...if i press esc and open game window again fps drops go off for 1-2 hours again, what the....?

Could be some kind of power saving feature kicking in, as refraction recommended try checking the temperatures and maybe clock speeds when you get those slowdowns, you can check them with an app like CoreTemp.

Would also help if you told us the EE/GS% numbers in the game window when you get the problem.